Condition-specific 3’ mRNA isoform half-lives and stability elements in yeast
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PROVIDER: PRJNA948348 | ENA |
REPOSITORIES: ENA
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Project description:Alternative polyadenylation generates numerous 3’ mRNA isoforms that can differ in their stability, structure, and function. These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3’ untranslated regions (3’UTRs). Here, we examine how environmental conditions affect 3’ mRNA isoform turnover and structure in yeast cells on a transcriptome scale. Isoform stability broadly increases when cells grow more slowly, with relative half-lives of most isoforms being well correlated across multiple conditions. Surprisingly, dimethyl sulfate probing reveals that individual 3’ isoforms have similar structures across different conditions, in contrast to the extensive structural differences that can exist between closely related isoforms in an individual condition. Unexpectedly, most mRNA stabilizing and destabilizing elements function only in a single growth condition. The genes associated with some classes of condition-specific stability elements are enriched for different functional categories, suggesting that regulated mRNA stability might contribute to adaptation to different growth environments. Condition-specific stability elements do not result in corresponding condition-specific changes in steady-state mRNA isoform levels. This observation is consistent with a compensatory mechanism between polyadenylation and stability, and it suggests that condition-specific mRNA stability elements might largely reflect condition-specific regulation of mRNA 3’ end formation.
2023-06-01 | GSE228123 | GEO
Project description:We measured half-lives of 21,248 mRNA 3’ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, the half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A) binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilization and stabilization elements are linked to the degree to which the poly(A) tail can engage in double-stranded structures. Isoforms engineered to fold into 3’ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at the 3’ ends are a major determinant of mRNA stability. Half-lives of 21,248 mRNA 3’ isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process.
2014-04-02 | E-GEOD-52286 | biostudies-arrayexpress
Project description:We measured half-lives of 21,248 mRNA 3’ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, the half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A) binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilization and stabilization elements are linked to the degree to which the poly(A) tail can engage in double-stranded structures. Isoforms engineered to fold into 3’ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at the 3’ ends are a major determinant of mRNA stability.
2014-04-02 | GSE52286 | GEO
Project description:Alternative polyadenylation generates numerous 3' mRNA isoforms that can differ in their stability, structure, and function. These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3' untranslated regions (3'UTRs). Here, we examine how environmental conditions affect 3' mRNA isoform turnover and structure in yeast cells on a transcriptome scale. Isoform stability broadly increases when cells grow more slowly, with relative half-lives of most isoforms being well correlated across multiple conditions. Surprisingly, dimethyl sulfate probing reveals that individual 3' isoforms have similar structures across different conditions, in contrast to the extensive structural differences that can exist between closely related isoforms in an individual condition. Unexpectedly, most mRNA stabilizing and destabilizing elements function only in a single growth condition. The genes associated with some classes of condition-specific stability elements are enriched for different functional categories, suggesting that regulated mRNA stability might contribute to adaptation to different growth environments. Condition-specific stability elements do not result in corresponding condition-specific changes in steady-state mRNA isoform levels. This observation is consistent with a compensatory mechanism between polyadenylation and stability, and it suggests that condition-specific mRNA stability elements might largely reflect condition-specific regulation of mRNA 3' end formation.
| S-EPMC10161003 | biostudies-literature
Project description:Global RNA half lives in cyanobacteria
| PRJNA429921 | ENA
Project description:We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.
2019-01-01 | GSE109174 | GEO
Project description:This work aimed at analysing mRNA half lives in drug resistant and in drug sensitive strains of C. albicans (Gu4 and Gu5 azole susceptible and resistant clinical isolates (franz et al., 1999)), using the transcriptional inhibitor thiolutine.
2011-10-01 | E-TABM-1179 | biostudies-arrayexpress
Project description:We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay.
2017-09-06 | GSE103467 | GEO
Project description:Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff
| PRJNA661297 | ENA
Project description:Determining mRNA half-lives on a transcriptome-wide scale
| PRJNA416702 | ENA